{"title"=>"A pH sensitive high-throughput assay for miRNA binding of a peptide-aminoglycoside (PA) library", "type"=>"journal", "authors"=>[{"first_name"=>"Derrick", "last_name"=>"Watkins", "scopus_author_id"=>"55430752900"}, {"first_name"=>"Liuwei", "last_name"=>"Jiang", "scopus_author_id"=>"56431703200"}, {"first_name"=>"Smita", "last_name"=>"Nahar", "scopus_author_id"=>"56118250800"}, {"first_name"=>"Souvik", "last_name"=>"Maiti", "scopus_author_id"=>"7202014988"}, {"first_name"=>"Dev P.", "last_name"=>"Arya", "scopus_author_id"=>"7004803271"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0144251", "issn"=>"19326203", "sgr"=>"84957108770", "scopus"=>"2-s2.0-84957108770", "pui"=>"607918471", "pmid"=>"26656788", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"53a74dcb-105b-3b47-b9fa-dbd0ccc5a4f7", "abstract"=>"MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC50 for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.", "link"=>"http://www.mendeley.com/research/ph-sensitive-highthroughput-assay-mirna-binding-peptideaminoglycoside-pa-library", "reader_count"=>7, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>1, "Other"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>1, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Belgium"=>1}, "group_count"=>0}

{"files"=>["https://ndownloader.figshare.com/files/2606938"], "description"=>"<p>The preliminary miRNA (pre-miRNA) containing the mature 5’ (red) or 3’ (blue) strand is transported out of the nucleus by exportan5 in complex with RAN•GTP, and released into the cytoplasm. The pre-miRNA is cleaved by the endonuclease III, Dicer, to produce the mature duplex miRNA of ~22 bases per strand. The mature duplex miRNA is then loaded onto a argonaute (AGO) protein where it is unwound, the passenger strand is released, and the guide strand is arranged in the A-form conformation (modelled here as either or both the 5’ and 3’ strand is used as the guide strand). The target mRNA (lime green or magenta) is bound to the complex, resulting the suppression of its translation and protein synthesis. EXP5 (green) was modelled from PDB id:3A6P, Dicer (purple) was from PDB id:4NH5, and AGO (brown) was modelled from PDB id:4W5R.</p>", "links"=>[], "tags"=>["binding sites", "pa", "miRNA binding compounds", "throughput displacement assay", "affinity", "ic", "bind miRNA"], "article_id"=>1623522, "categories"=>["Biological Sciences"], "users"=>["Derrick Watkins", "Liuwei Jiang", "Smita Nahar", "Souvik Maiti", "Dev P. Arya"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0144251.g001", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_of_miRNA_processing_/1623522", "title"=>"Schematic of miRNA processing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-17 08:08:28"}

{"files"=>["https://ndownloader.figshare.com/files/2606949", "https://ndownloader.figshare.com/files/2606950", "https://ndownloader.figshare.com/files/2606951", "https://ndownloader.figshare.com/files/2606952", "https://ndownloader.figshare.com/files/2606953", "https://ndownloader.figshare.com/files/2606954", "https://ndownloader.figshare.com/files/2606955", "https://ndownloader.figshare.com/files/2606956", "https://ndownloader.figshare.com/files/2606957"], "description"=>"<div><p>MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC<sub>50</sub> for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.</p></div>", "links"=>[], "tags"=>["binding sites", "pa", "miRNA binding compounds", "throughput displacement assay", "affinity", "ic", "bind miRNA"], "article_id"=>1623533, "categories"=>["Biological Sciences"], "users"=>["Derrick Watkins", "Liuwei Jiang", "Smita Nahar", "Souvik Maiti", "Dev P. Arya"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0144251.s001", "https://dx.doi.org/10.1371/journal.pone.0144251.s002", "https://dx.doi.org/10.1371/journal.pone.0144251.s003", "https://dx.doi.org/10.1371/journal.pone.0144251.s004", "https://dx.doi.org/10.1371/journal.pone.0144251.s005", "https://dx.doi.org/10.1371/journal.pone.0144251.s006", "https://dx.doi.org/10.1371/journal.pone.0144251.s007", "https://dx.doi.org/10.1371/journal.pone.0144251.s008", "https://dx.doi.org/10.1371/journal.pone.0144251.s009"], "stats"=>{"downloads"=>12, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_pH_Sensitive_High_Throughput_Assay_for_miRNA_Binding_of_a_Peptide_Aminoglycoside_PA_Library_/1623533", "title"=>"A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-12-17 08:08:29"}